--- title: "GGIR configuration parameters" output: html_document: toc : true number_sections: true toc_depth: 3 toc_float: true #by turning this on, the table of contents moves to the left of the page. urlcolor: blue vignette: > %\VignetteIndexEntry{GGIR configuration parameters} \usepackage[utf8]{inputenc} %\VignetteEngine{knitr::rmarkdown} --- **NOTE: If you are viewing this page via CRAN note that the main GGIR documentation has been migrated to the [GGIR GitHub pages](https://wadpac.github.io/GGIR/).** The GGIR [shell function](https://cran.r-project.org/package=GGIR/vignettes/GGIR.html#23_GGIR_shell_function) takes the input arguments and groups them into parameter objects. The first section below displays all optional GGIR input argument names, the GGIR part (1, 2, 3, 4 and/or 5) they are used in, and the parameter object they are stored in. As you will see, a few parameters are not part of any parameter object because they are direct arguments of the GGIR shell function. In the [second section of this vignette](#default-argument-values) you will find a description and default value for all the arguments. # Input arguments/parameters overview | Argument (parameter) | Used in GGIR part | Parameter object | |-----------------------------|-------------------|--------------------------| | datadir | 1, 2, 4, 5 | not in parameter objects | | f0 | 1, 2, 3, 4, 5 | not in parameter objects | | f1 | 1, 2, 3, 4, 5 | not in parameter objects | | windowsizes | 1, 5 | params_general | | desiredtz | 1, 2, 3, 4, 5 | params_general | | overwrite | 1, 2, 3, 4, 5 | params_general | | do.parallel | 1, 2, 3, 5 | params_general | | maxNcores | 1, 2, 3, 5 | params_general | | use_trycatch_serial | 1, 2, 3, 5, 6 | params_general | | myfun | 1, 2, 3 | not in parameter objects | | outputdir | 1 | not in parameter objects | | studyname | 1 | not in parameter objects | | chunksize | 1 | params_rawdata | | do.enmo | 1 | params_metrics | | do.lfenmo | 1 | params_metrics | | do.en | 1 | params_metrics | | do.bfen | 1 | params_metrics | | do.hfen | 1 | params_metrics | | do.hfenplus | 1 | params_metrics | | do.mad | 1 | params_metrics | | do.anglex | 1 | params_metrics | | do.angley | 1 | params_metrics | | do.angle | 1 | params_metrics | | do.enmoa | 1 | params_metrics | | do.roll_med_acc_x | 1 | params_metrics | | do.roll_med_acc_y | 1 | params_metrics | | do.roll_med_acc_z | 1 | params_metrics | | do.dev_roll_med_acc_x | 1 | params_metrics | | do.dev_roll_med_acc_y | 1 | params_metrics | | do.dev_roll_med_acc_z | 1 | params_metrics | | do.lfen | 1 | params_metrics | | do.lfx | 1 | params_metrics | | do.lfy | 1 | params_metrics | | do.lfz | 1 | params_metrics | | do.hfx | 1 | params_metrics | | do.hfy | 1 | params_metrics | | do.hfz | 1 | params_metrics | | do.bfx | 1 | params_metrics | | do.bfy | 1 | params_metrics | | do.bfz | 1 | params_metrics | | do.zcx | 1 | params_metrics | | do.zcy | 1 | params_metrics | | do.zcz | 1 | params_metrics | | do.neishabouricounts | 1 | params_metrics | | actilife_LFE | 1 | params_metrics | | lb | 1 | params_metrics | | hb | 1 | params_metrics | | n | 1 | params_metrics | | do.cal | 1 | params_rawdata | | spherecrit | 1 | params_rawdata | | minloadcrit | 1 | params_rawdata | | printsummary | 1 | params_rawdata | | print.filename | 1 | params_general | | backup.cal.coef | 1 | params_rawdata | | rmc.noise | 1 | params_rawdata | | rmc.dec | 1 | params_rawdata | | rmc.firstrow.acc | 1 | params_rawdata | | rmc.firstrow.header | 1 | params_rawdata | | rmc.col.acc | 1 | params_rawdata | | rmc.col.temp | 1 | params_rawdata | | rmc.col.time | 1 | params_rawdata | | rmc.unit.acc | 1 | params_rawdata | | rmc.unit.temp | 1 | params_rawdata | | rmc.origin | 1 | params_rawdata | | rmc.header.length | 1 | params_rawdata | | rmc.format.time | 1 | params_rawdata | | rmc.bitrate | 1 | params_rawdata | | rmc.dynamic_range | 1 | params_rawdata | | rmc.unsignedbit | 1 | params_rawdata | | rmc.desiredtz | 1 | params_rawdata | | rmc.sf | 1 | params_rawdata | | rmc.headername.sf | 1 | params_rawdata | | rmc.headername.sn | 1 | params_rawdata | | rmc.headername.recordingid | 1 | params_rawdata | | rmc.header.structure | 1 | params_rawdata | | rmc.check4timegaps | 1 | params_rawdata | | rmc.col.wear | 1 | params_rawdata | | rmc.doresample | 1 | params_rawdata | | imputeTimegaps | 1 | params_rawdata | | dayborder | 1, 2, 5 | params_general | | dynrange | 1 | params_rawdata | | nonwear_range_threshold | 1 | params_rawdata | | configtz | 1 | params_general | | minimumFileSizeMB | 1 | params_rawdata | | interpolationType | 1 | params_rawdata | | expand_tail_max_hours | deprecated | params_general | | recordingEndSleepHour | 1 | params_general | | maxRecordingInterval | 1 | params_general | | recording_split_times | 1 | params_general | | recording_split_overlap | 1 | params_general | | recording_split_ignore_edges | 1 | params_general | | recording_split_timeformat | 1 | params_general | | nonwear_approach | 1 | params_general | | dataFormat | 1 | params_general | | extEpochData_timeformat | 1 | params_general | | metadatadir | 2, 3, 4, 5 | not in parameter objects | | minimum_MM_length.part5 | 5 | params_cleaning | | strategy | 2, 5 | params_cleaning | | hrs.del.start | 2, 5 | params_cleaning | | hrs.del.end | 2, 5 | params_cleaning | | maxdur | 2, 5 | params_cleaning | | max_calendar_days | 2 | params_cleaning | | includedaycrit | 2, 5 | params_cleaning | | nonWearEdgeCorrection | 2 | params_cleaning | | nonwearFiltermaxHours | 2 | params_cleaning | | nonwearFilterWindow | 2 | params_cleaning | | L5M5window | 2 | params_247 | | M5L5res | 2, 5 | params_247 | | winhr | 2, 5 | params_247 | | qwindow | 2 | params_247 | | qlevels | 2 | params_247 | | ilevels | 2 | params_247 | | mvpathreshold | 2 | params_phyact | | boutcriter | 2 | params_phyact | | ndayswindow | 2 | params_cleaning | | idloc | 2, 4 | params_general | | do.imp | 2 | params_cleaning | | storefolderstructure | 2, 4, 5 | params_output | | epochvalues2csv | 2 | params_output | | do.part2.pdf | 2 | params_output | | sep_reports | 2, 4, 5 | params_output | | dec_reports | 2, 4, 5 | params_output | | sep_config | 1, 2, 3, 4, 5 | params_output | | dec_config | 1, 2, 3, 4, 5 | params_output | | mvpadur | 2 | params_phyact | | bout.metric | 2, 5 | params_phyact | | closedbout | 2 | params_phyact | | IVIS_windowsize_minutes | 2 | params_247 | | IVIS_epochsize_seconds | 2 | params_247 | | IVIS.activity.metric | 2 | params_247 | | iglevels | 2, 5 | params_247 | | TimeSegments2ZeroFile | 2 | params_cleaning | | qM5L5 | 2 | params_247 | | MX.ig.min.dur | 2 | params_247 | | qwindow_dateformat | 2 | params_247 | | part2CR | 2 | params_247 | | anglethreshold | 3 | params_sleep | | timethreshold | 3 | params_sleep | | ignorenonwear | 3 | params_sleep | | HDCZA_threshold | 3 | params_sleep | | acc.metric | 3, 5 | params_general | | do.part3.pdf | 3 | params_output | | sensor.location | 3, 4 | params_general | | HASPT.algo | 3 | params_sleep | | HASIB.algo | 3 | params_sleep | | Sadeh_axis | 3 | params_sleep | | longitudinal_axis | 3 | params_sleep | | HASPT.ignore.invalid | 3 | params_sleep | | oakley_threshold | 3 | params_sleep | | consider_marker_button | 3 | params_sleep | | impute_marker_button | 3 | params_sleep | | SRI1_smoothing_wsize_hrs | 3 | params_sleep | | SRI1_smoothing_frac | 3 | params_sleep | | spt_min_block_dur | 3 | params_sleep | | spt_max_gap_dur | 3 | params_sleep | | spt_max_gap_ratio | 3 | params_sleep | | HorAngle_threshold | 3 | params_sleep | | guider_cor_maxgap_hrs | 3 | params_sleep | | guider_cor_min_frac_sib | 3 | params_sleep | | guider_cor_min_hrs | 3 | params_sleep | | guider_cor_meme_frac_out | 3 | params_sleep | | guider_cor_meme_frac_in | 3 | params_sleep | | guider_cor_meme_min_hrs | 3 | params_sleep | | guider_cor_do | 3 | params_sleep | | guider_cor_meme_min_dys | 3 | params_sleep | | loglocation | 4, 5 | params_sleep | | colid | 4 | params_sleep | | coln1 | 4 | params_sleep | | do.visual | 4 | params_output | | outliers.only | 4 | params_output | | excludefirstlast | 4 | params_cleaning | | criterror | 4 | params_output | | includenightcrit | 4 | params_cleaning | | relyonguider | 4 | params_sleep | | relyonsleeplog | 4 | deprecated | | sleepefficiency.metric | 4 | params_sleep | | def.noc.sleep | 4 | params_sleep | | sib_must_fully_overlap_with_TimeInBed | 4 | params_sleep | | data_cleaning_file | 4, 5 | params_cleaning | | excludefirst.part4 | 4 | params_cleaning | | excludelast.part4 | 4 | params_cleaning | | sleepwindowType | 4 | params_cleaning | | excludefirstlast.part5 | 5 | params_cleaning | | boutcriter.mvpa | 5 | params_phyact | | boutcriter.in | 5 | params_phyact | | boutcriter.lig | 5 | params_phyact | | threshold.lig | 5 | params_phyact | | threshold.mod | 5 | params_phyact | | threshold.vig | 5 | params_phyact | | boutdur.mvpa | 5 | params_phyact | | boutdur.in | 5 | params_phyact | | boutdur.lig | 5 | params_phyact | | save_ms5rawlevels | 5 | params_output | | part5_agg2_60seconds | 5 | params_general | | includedaycrit.part5 | 5 | params_cleaning | | includenightcrit.part5 | 5 | params_cleaning | | frag.metrics | 5 | params_phyact | | LUXthresholds | 5 | params_247 | | LUX_cal_constant | 5 | params_247 | | LUX_cal_exponent | 5 | params_247 | | LUX_day_segments | 5 | params_247 | | SRI2_WASOmin | 5 | params_247 | | timewindow | 5 | params_output | | save_ms5raw_format | 5 | params_output | | save_ms5raw_without_invalid | 5 | params_output | | do.sibreport | 5 | params_output | | possible_nap_window | 5 | params_sleep | | possible_nap_dur | 5 | params_sleep | | possible_nap_gap | 5 | params_sleep | | nap_markerbutton_method | 5 | params_sleep | | nap_markerbutton_max_distance | 5 | params_sleep | | method_research_vars | 5 | params_sleep | | includecrit.part6 | 6 | params_cleaning | | part6_threshold_combi | 6 | params_phyact | | part6CR | 6 | params_247 | | part6HCA | 6 | params_247 | | part6Window | 6 | params_247 | | part6DFA | 6 | params_247 | | require_complete_lastnight_part5 | 5 | params_output | | visualreport_without_invalid| visualreport | params_output | | visualreport_hrsPerRow | visualreport | params_output | | visualreport_focus | visualreport | params_output | | visualreport_validcrit | visualreport | params_output | | dofirstpage | visualreport | params_output | | visualreport | visualreport | params_output | | viewingwindow | visualreport | params_output | # Arguments/parameters description {#default-argument-values} All information as shown below has been auto-generated and is identical to the information provided in the [GGIR package pdf manual](https://CRAN.R-project.org/package=GGIR/GGIR.pdf). ## GGIR function input arguments ### mode {-} `r format(GGIR::ShellDoc2Vignette("mode"))` ### datadir {-} `r format(GGIR::ShellDoc2Vignette("datadir"))` ### outputdir {-} `r format(GGIR::ShellDoc2Vignette("outputdir"))` ### studyname {-} `r format(GGIR::ShellDoc2Vignette("studyname"))` ### f0 {-} `r format(GGIR::ShellDoc2Vignette("f0"))` ### f1 {-} `r format(GGIR::ShellDoc2Vignette("f1"))` ### do.report {-} `r format(GGIR::ShellDoc2Vignette("do.report"))` ### configfile {-} `r format(GGIR::ShellDoc2Vignette("configfile"))` ### myfun {-} `r format(GGIR::ShellDoc2Vignette("myfun"))` ## General Parameters `r format(GGIR::parametersVignette("general"))` ## Raw Data Parameters `r format(GGIR::parametersVignette("rawdata"))` ## Metrics Parameters `r format(GGIR::parametersVignette("metrics"))` ## Cleaning Parameters `r format(GGIR::parametersVignette("cleaning"))` ## Sleep Parameters `r format(GGIR::parametersVignette("sleep"))` ## Physical activity Parameters `r format(GGIR::parametersVignette("phyact"))` ## 24/7 Parameters `r format(GGIR::parametersVignette("247"))` ## Output Parameters `r format(GGIR::parametersVignette("output"))` ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` ```{r, echo=FALSE, out.width = "60%", out.extra='style="border: 0; padding:20px"', fig.alt="GGIR logo"} knitr::include_graphics("GGIR-MASTERLOGO-RGB.png") ```